The last major accident in Indonesia was in December 2014 when an AirAsia Indonesia's Airbus A320 aircraft crashed into the waters after taking off from Surabaya to Singapore with 162 people on board.
Authorities are sending recovered remains to hospital for DNA comparison to passengers' relatives.
The issue was checked by maintenance workers overnight before the plane was cleared for the ill-fated flight, the airline said. "The captain said the problem was resolved and he made a decision to continue the trip to Jakarta".
Herson, the chief of the airport authority for the Bali and Nusa Tenggara area, told Reuters that after the call, the pilot updated the control tower to say that the plane was flying normally and that he would not return to the airport as requested.
The Denpasar-Jakarta flight landed at the Indonesian capital's airport at 10:55pm local time on Sunday.
Divers recovered the crashed jet's flight data recorder from the seafloor on Thursday, a crucial development in the investigation into what caused the 2-month-old plane to plunge into Indonesian seas earlier this week, killing all of its passengers.
Data from flight-tracking sites show the plane had erratic speed and altitude in the early minutes of a flight on Sunday and on its fatal flight on Monday.
The Lion Air aircraft which crashed into the Java Sea reportedly had technical problems prior to takeoff the day before.
The data recorder was reportedly found in almost 100 feet of water about 1,600 feet from where the jet lost contact.
Two passengers from Sunday's flight posted on Instagram reporting they had been concerned about problems with the air conditioning system and cabin lighting before the plane left Bali almost three hours late.
It was the worst airline disaster in Indonesia in more than two decades and renewed concerns about safety in its fast-growing aviation industry, which was recently removed from European Union and US blacklists.
Items fished out of the sea showed wallets and other personal effects, including a child's Hello Kitty purse. Divers were deployed into the ocean to find the plane's black box.
In wake of the tragedy, Indonesia has directed the inspection of all Boeing 737 Max 8 planes belonging to commercial airlines in the country.
Officials displayed one of the jet's two flight recorders at a news conference Thursday evening, later confirmed to be the flight data recorder, and said they would immediately attempt to download information and begin an analysis.
Mr Satmiko pointed to the device's poor condition as evidence of the "extraordinary impact" of the crash.
Investigators have also found the flight data recorder, the "black box", from Lion Air Flight JT610.
A ping detector was used by the search team to locate signals from the black box, along with a remotely operated underwater vehicle (ROV). The downloading of the data will take three weeks.
The results from a preliminary investigation will be made public after 30 days, another KNKT official said.
But hopes are fading of finding a large section of fuselage intact with bodies, easily retrievable, inside.
"What is important for us is to get more information about the victims because having their remains back is important for us so we can bury them properly", said Ade Inyo, whose brother-in-law was on the flight.
Ningsi Ayorbaba weeps as she await news of her husband Paul Ferdinan Ayorbaba, a victim of Lion Air flight JT610.
He told the U.S. news outlet the plane felt as if it was "struggling to ascend" before it suddenly dropped "as if it was losing power". An airplane has two recorders: one that captures flight data such as readings from electronic systems, and another that records the pilot and co-pilot in the cockpit.
The nation's transport ministry said it will step up checks on aircraft and ground planes with technical snags that can't be solved.
Lion Air said the aircraft that crashed had been airworthy and the pilot and co-pilot had 11,000 hours of flying time between them.
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